Increasing scarcity of good quality water in many arid and semi-arid regions necessitates the use of poor quality groundwater for irrigation. Soil degradation resulting from alkali water irrigation has become a serious threat to soil health. In the present study, we conducted an investigation (2021-22) on the physicochemical properties (soil organic carbon, available Na, and available K) of sandy loam soil under a semi-controlled lysimeter. Wheat was grown as an experimental crop, which was irrigated with synthetic alkali waters having similar salts (total electrolyte concentration, TEC = 30 me L−1) and sodium adsorption ratio (SARiw 10 mmol L−1) but varying in residual sodium carbonate (RSC) are being continuously applied since 2004 (20 years). Five types of irrigation water having different levels of residual sodium carbonate comprised. (T1) best available groundwater, (T2) residual sodium carbonate water 1 (RSC- 5 me L–1), (T3) RSC water 2 (RSC 10 me L–1), (T4) RSC water 3 [RSC 10 treated with gypsum (RSC 10 neutralized to RSC 5 me L–1 with gypsum)] and (T5) RSC water 4 [RSC 10 treated with sulphur (RSC 10 neutralized to RSC 5 me L–1 with sulphur)]. Soil samples were collected after harvesting two wheat varieties (KRL 210 and HD 3226). Long-term irrigations with alkali water increased the available Na and K in the soil. Furthermore, soil organic carbon (SOC) decreased significantly with increasing alkalinity of irrigation water. Continuous irrigation with alkali water reduced grain yield of wheat by 31.7% over BAW. Moreover, the addition of gypsum and sulphuric acid has shown some capacity to partially restore soil properties, although not to the level of BAW. The majority of soil parameters under both crop cultivars showed a similar trend. The study's findings led to the conclusion that continuous applications of alkali water drastically degrade soil physicochemical properties. Partial neutralization of alkali water did not allow for the sustained existence of soil physicochemical properties. Consequently, it is recommended that the rate at which amendments are added to alkali water be adjusted to restore the decline in soil physicochemical properties.